Update documentation website (long overdue)

Merge branch 'RELEASE_3_22' into documentation-devel

# Conflicts:
#	DESCRIPTION

Author: lambdamoses

.github/workflows/R-CMD-check.yaml

@@ -35,7 +35,7 @@ jobs:
       - uses: r-lib/actions/setup-pandoc@v2
 
       - if: runner.os == 'macOS'
-        run: brew install apache-arrow
+        run: brew install apache-arrow fftw jpeg-turbo libtiff imagemagick pkg-config
 
       - name: Setup R and Bioconductor
         uses: grimbough/bioc-actions/setup-bioc@v1

.gitignore

@@ -5,3 +5,4 @@
 *.Rproj
 inst/doc
 docs
+.DS_Store

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: SpatialFeatureExperiment
 Type: Package
 Title: Integrating SpatialExperiment with Simple Features in sf
-Version: 1.7.1
+Version: 1.12.1
 Authors@R: 
-    c(person("Lambda", "Moses", email = "dlu2@caltech.edu", 
+    c(person("Lambda", "Moses", email = "dl3764@columbia.edu", 
     role = c("aut", "cre"),
     comment = c(ORCID = "0000-0002-7092-9427")),
     person("Alik", "Huseynov",
@@ -20,7 +20,7 @@ Description: A new S4 class integrating Simple Features with the R package sf
     be used.
 Imports:
     Biobase,
-    BiocGenerics,
+    BiocGenerics (>= 0.51.2),
     BiocNeighbors,
     BiocParallel,
     data.table,
@@ -37,6 +37,7 @@ Imports:
     sfheaders,
     SingleCellExperiment,
     SpatialExperiment,
+    spatialreg,
     spdep (>= 1.1-7),
     SummarizedExperiment,
     stats,
@@ -45,7 +46,7 @@ Imports:
     zeallot
 License: Artistic-2.0
 Encoding: UTF-8
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Collate: 
     'AllGenerics.R'
     'utils.R'
@@ -57,6 +58,7 @@ Collate:
     'changeSampleIDs.R'
     'coerce.R'
     'data.R'
+    'debris.R'
     'df2sf.R'
     'dimGeometries.R'
     'featureData.R'
@@ -66,20 +68,24 @@ Collate:
     'image.R'
     'int_dimData.R'
     'internal-Voyager.R'
+    'listw2sparse.R'
     'localResults.R'
     'read.R'
     'reexports.R'
     'saveRDS.R'
     'spatialGraphs.R'
     'split.R'
     'subset.R'
+    'tissue_boundary.R'
     'transformation.R'
     'updateObject.R'
     'validity.R'
+    'zzz.R'
 Suggests: 
     arrow,
     BiocStyle,
     dplyr,
+    gmp,
     knitr,
     RBioFormats,
     rhdf5,
@@ -92,10 +98,12 @@ Suggests:
     sparseMatrixStats,
     testthat (>= 3.0.0),
     tidyr,
-    Voyager,
+    VisiumIO,
+    Voyager (>= 1.7.2),
+    withr,
     xml2
 Remotes:
-    Voyager=github::pachterlab/voyager
+    Voyager=github::pachterlab/voyager@devel
 Config/testthat/edition: 3
 Depends: 
     R (>= 4.2.0)

NAMESPACE

@@ -40,6 +40,7 @@ export("txSpots<-")
 export(.check_features)
 export(.check_rg)
 export(.check_sample_id)
+export(.ext_)
 export(.rm_empty_geometries)
 export(.symbol2id)
 export(.value2df)
@@ -89,8 +90,10 @@ export(df2sf)
 export(dimGeometries)
 export(dimGeometry)
 export(dimGeometryNames)
+export(findDebrisCells)
 export(findSpatialNeighbors)
 export(findVisiumGraph)
+export(findVisiumHDGraph)
 export(formatTxSpots)
 export(formatTxTech)
 export(gdalParquetAvailable)
@@ -99,6 +102,8 @@ export(getImg)
 export(getParams)
 export(getPixelSize)
 export(getTechTxFields)
+export(getTissueBoundaryConcave)
+export(getTissueBoundaryImg)
 export(imageIDs)
 export(imgData)
 export(imgRaster)
@@ -112,11 +117,13 @@ export(localResults)
 export(logcounts)
 export(mirror)
 export(mirrorImg)
+export(multi_listw2sparse)
 export(nucSeg)
 export(origin)
 export(read10xVisiumSFE)
 export(readCosMX)
 export(readSelectTx)
+export(readVisiumHD)
 export(readVizgen)
 export(readXenium)
 export(reducedDim)
@@ -142,6 +149,7 @@ export(spatialGraph)
 export(spatialGraphNames)
 export(spatialGraphs)
 export(splitByCol)
+export(splitComponent)
 export(splitContiguity)
 export(splitSamples)
 export(spotPoly)
@@ -187,12 +195,14 @@ exportMethods(annotGeometry)
 exportMethods(annotGeometryNames)
 exportMethods(bbox)
 exportMethods(cbind)
+exportMethods(containsOutOfMemoryData)
 exportMethods(cropImg)
 exportMethods(dim)
 exportMethods(dimGeometries)
 exportMethods(dimGeometry)
 exportMethods(dimGeometryNames)
 exportMethods(ext)
+exportMethods(findDebrisCells)
 exportMethods(findSpatialNeighbors)
 exportMethods(imgRaster)
 exportMethods(imgSource)
@@ -225,6 +235,8 @@ importClassesFrom(SpatialExperiment,SpatialExperiment)
 importClassesFrom(SpatialExperiment,VirtualSpatialImage)
 importClassesFrom(terra,SpatRaster)
 importFrom(BiocGenerics,cbind)
+importFrom(BiocGenerics,containsOutOfMemoryData)
+importFrom(BiocGenerics,saveRDS)
 importFrom(BiocGenerics,updateObject)
 importFrom(BiocNeighbors,AnnoyParam)
 importFrom(BiocNeighbors,KmknnParam)
@@ -235,18 +247,26 @@ importFrom(BiocParallel,bplapply)
 importFrom(BiocParallel,bpmapply)
 importFrom(DropletUtils,read10xCounts)
 importFrom(EBImage,Image)
+importFrom(EBImage,closing)
+importFrom(EBImage,fillHull)
+importFrom(EBImage,makeBrush)
+importFrom(EBImage,normalize)
+importFrom(EBImage,otsu)
 importFrom(Matrix,colSums)
 importFrom(Matrix,rowSums)
 importFrom(Matrix,sparseMatrix)
+importFrom(S4Vectors,"mcols<-")
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,SimpleList)
 importFrom(S4Vectors,combineCols)
 importFrom(S4Vectors,isEmpty)
 importFrom(S4Vectors,make_zero_col_DFrame)
+importFrom(S4Vectors,mcols)
 importFrom(S4Vectors,metadata)
 importFrom(S4Vectors,setValidity2)
 importFrom(S4Vectors,showAsCell)
+importFrom(S4Vectors,split)
 importFrom(SingleCellExperiment,"altExp<-")
 importFrom(SingleCellExperiment,"int_colData<-")
 importFrom(SingleCellExperiment,"int_elementMetadata<-")
@@ -267,14 +287,14 @@ importFrom(SingleCellExperiment,reducedDimNames)
 importFrom(SingleCellExperiment,reducedDims)
 importFrom(SpatialExperiment,"imgData<-")
 importFrom(SpatialExperiment,"spatialCoords<-")
+importFrom(SpatialExperiment,"spatialCoordsNames<-")
 importFrom(SpatialExperiment,SpatialExperiment)
 importFrom(SpatialExperiment,addImg)
 importFrom(SpatialExperiment,getImg)
 importFrom(SpatialExperiment,imgData)
 importFrom(SpatialExperiment,imgRaster)
 importFrom(SpatialExperiment,imgSource)
 importFrom(SpatialExperiment,mirrorImg)
-importFrom(SpatialExperiment,read10xVisium)
 importFrom(SpatialExperiment,rmvImg)
 importFrom(SpatialExperiment,rotateImg)
 importFrom(SpatialExperiment,spatialCoords)
@@ -287,6 +307,7 @@ importFrom(SummarizedExperiment,assayNames)
 importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
+importFrom(data.table,":=")
 importFrom(data.table,as.data.table)
 importFrom(data.table,fread)
 importFrom(data.table,is.data.table)
@@ -313,7 +334,11 @@ importFrom(methods,slot)
 importFrom(methods,slotNames)
 importFrom(methods,validObject)
 importFrom(rjson,fromJSON)
+importFrom(rlang,"!!")
+importFrom(rlang,"%||%")
+importFrom(rlang,.data)
 importFrom(rlang,check_installed)
+importFrom(rlang,sym)
 importFrom(sf,"st_agr<-")
 importFrom(sf,"st_geometry<-")
 importFrom(sf,st_agr)
@@ -326,7 +351,7 @@ importFrom(sf,st_cast)
 importFrom(sf,st_centroid)
 importFrom(sf,st_collection_extract)
 importFrom(sf,st_coordinates)
-importFrom(sf,st_covered_by)
+importFrom(sf,st_covers)
 importFrom(sf,st_disjoint)
 importFrom(sf,st_distance)
 importFrom(sf,st_drop_geometry)
@@ -349,6 +374,7 @@ importFrom(sf,st_polygon)
 importFrom(sf,st_read)
 importFrom(sf,st_sf)
 importFrom(sf,st_sfc)
+importFrom(sf,st_simplify)
 importFrom(sf,st_union)
 importFrom(sf,st_z_range)
 importFrom(sf,st_zm)
@@ -357,12 +383,15 @@ importFrom(sfheaders,sf_multilinestring)
 importFrom(sfheaders,sf_multipoint)
 importFrom(sfheaders,sf_multipolygon)
 importFrom(sfheaders,sf_polygon)
+importFrom(spatialreg,as_dgRMatrix_listw)
 importFrom(spdep,card)
 importFrom(spdep,dnearneigh)
 importFrom(spdep,gabrielneigh)
 importFrom(spdep,graph2nb)
 importFrom(spdep,knearneigh)
 importFrom(spdep,knn2nb)
+importFrom(spdep,mat2listw)
+importFrom(spdep,n.comp.nb)
 importFrom(spdep,nb2listw)
 importFrom(spdep,nb2listwdist)
 importFrom(spdep,poly2nb)
@@ -374,6 +403,7 @@ importFrom(stats,median)
 importFrom(stats,na.omit)
 importFrom(stats,setNames)
 importFrom(terra,"ext<-")
+importFrom(terra,as.raster)
 importFrom(terra,ext)
 importFrom(terra,inMemory)
 importFrom(terra,nlyr)
@@ -389,4 +419,5 @@ importFrom(utils,getFromNamespace)
 importFrom(utils,head)
 importFrom(utils,packageVersion)
 importFrom(utils,read.csv)
+importFrom(utils,tail)
 importFrom(zeallot,"%<-%")

R/AllGenerics.R

@@ -232,6 +232,8 @@ setGeneric(".mirror_img", function(x, direction, bbox_all, ...) standardGeneric(
 
 setGeneric(".rotate_img", function(x, degrees, bbox_all, ...) standardGeneric(".rotate_img"))
 
+setGeneric(".scale_img", function(x, factor, bbox_all, ...) standardGeneric(".scale_img"))
+
 #' @export
 setGeneric("scaleImg", function(x, factor, ...) standardGeneric("scaleImg"))
 
@@ -244,7 +246,9 @@ setGeneric("affineImg", function(x, M, v, ...) standardGeneric("affineImg"))
 #' @export
 setGeneric("cropImg", function(x, bbox, ...) standardGeneric("cropImg"))
 
-if (!isGeneric("saveRDS")) {setGeneric("saveRDS", function (object, file="", ascii=FALSE, version=NULL, compress=TRUE, refhook=NULL) standardGeneric("saveRDS"))}
+if (!isGeneric("readRDS")) {
+    setGeneric("readRDS", function(file, refhook = NULL) standardGeneric("readRDS"))
+}
 
 #' @export
 setGeneric("toExtImage", function(x, ...) standardGeneric("toExtImage"))
@@ -272,3 +276,8 @@ setGeneric("Img<-", function(x, sample_id = 1L, image_id, scale_fct = 1, value)
 
 #' @export
 setGeneric("splitByCol", function(x, f, ...) standardGeneric("splitByCol"))
+
+#' @export
+setGeneric("findDebrisCells", function(x, max_cells = 5, distance_cutoff = 50,
+                                       BNPARAM = NULL, BPPARAM = SerialParam()) 
+    standardGeneric("findDebrisCells"))